Isekai harem fantasy is a good example of story vs setting as a conceptual framework.
Let's take Konasuba as an example because it's popular and one of the few isekai that I actually like. The STORY of Konasuba could be taking place in literally any setting. You could have Cyberpunk Konasuba in which Aqua is a jailbroken bootleg of a powerful AI, Darkness is an Adam Smasher tier cyborg who is basically invincible but also a masochist, and Megumin is a solo who blows all of her money on increasingly ludicrous single-shot missile launchers.
Okay. It would LITERALLY work exactly the same. You could do it in space, you could do it in a boxing setting, you could do it a sky-pirates setting like Skies of Arcadia, you could do it anywhere.
The SETTING of Konasuba isn't just boring, it's nonexistent. Everything that we know is in relation to the characters. Nothing else is really explained nor does it matter. If you just took the setting of Konasuba it would be indifferentiable from any of 10,000,000 basic D&D settings because it's just a blank canvass on which the characters who are the actual interest, are painted.
You can't make "isekai harem fantasy" as a setting, it's conceptually impossible, it's like making "Blood Meridian" as a setting. IT'S JUST THE SOUTHWEST IN THE 1850s. The thing that makes it "it" is the characters.